addition of contamination estimates into GLs

This is a first pass solution, and should probably not be used in production.
This commit is for future reference.
per-read group contamination estimates

This is a checkpoint.  This functionality is relatively stable.
partial haplotype observations

Use all read evidence, even when calling haplotypes, by utilizing equivalencies
between partial observations of a haplotype and the putative alleles at the
site.

Observations which partially support a number of haplotypes have their
probability mass divided amongst the alleles they support when calculating
genotype likelihoods.

This provision resolves sensitivity issues caused by
increased spanning coverage required to call small variants when using larger
--haplotype-length values.

The adjustment to genotype likelihood calculations currently requires the use
of the new GL calculation routine provided when enabling --prob-contamination
0, or providing a per-sample contamination estimate file via
--contamination-estimates.
Setting Release-Version v9.9.1
balanced observations for indels (indels)

For insertions (currently), require that the reference observations at the
haplotype containing the insertion flank the insertion by a combined number of
bases that is the same as the length of the insertion.

This normalizes the likelihood calculations for insertions.

Normalization is (currently) provided implicitly for deletions in that
reference bias prevents the mapping of longer deletions.  This effect is
stronger than the sum of bases effect driving bias problems for insertions.
add version_git.h
properly include Contamination.*
include autoversion in default build path

Now, the version will include the git commit id from the repo!
versioning fix (add version_git.h to dependencies)
updated .gitignore, added CNV BED example
parameter changes, --bam-list and --region

Allow a bam file list to be provided on the command line.

Allow the use of '-' as a region separator in region strings.
remove spurious N alleles from output

Now that haplotype construction occurs at every base, the removal of part-null
alleles needs to occur also in the genotypeAlleles routine (which establishes
which alleles should be used for genotyping).
updated bamtools
remove partial component from RO in VCF output
6x performance improvement

Remove duplicated genotype search, as the algorithm now always searches deeply.
The default default --pvar of 0 means "run gradient descent on everything".

Fix incorrect (too large type) usage of ttmath.  This resolves a major
performance bug (30% of runtime) in the previous builds.

Remove indel mask vector<bool>, whose aligned copy was occupying a large
fraction of runtime (50%).  Users employing this method for the removal of
artifacts are suggested to look at samtools BAQ, which applies an HMM to
incorporate local alignment quality into base quality.

Together, these changes increase processing speed in the 1000G release set
(2500 samples) by around 6x over the previous commit.
Setting Release-Version v9.9.2
update version_git.h
allow maximum search iterations to be == genotypingMaxIterations
Setting Release-Version v0.9.9.2
reset version to 0.9.9.2 (rather than v9...)